Bug Description

Bug:
After opening an application, sorting it in the launcher and then closing the application the icon disappears.

Solution:
After opening an application, it should be understood that sorting it means you want to keep it in the launcher. This option should be automatically checked after drag/dropping an icon that isn't already sent to stay. Note that if a user then chooses the option to un-pin the app icon from the Launcher, it position should still be remembered next time the app is started, see bug https://bugs.launchpad.net/ayatana-design/+bug/772517

Why this solution is better:
Typically, when a user sorts an icon it shows intent to keep the icon displayed among the others. This would also save the user one manual step of clicking "Keep in launcher" when they expect that to be the behavior of sorting.

With fixing this bug I believe it now enables us to bring back the upper accordion mode as well. Since launchers won't have the fixed position always which break the original argument to remove the upper accordion of the launcher.

Well, it would be possible, but it also seems that right-clicking an icon and un-stick it isn't a big deal, and it's just better to consider that as the configuration parameter, more than a generic option.